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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATCAGAGAGCTGATTTCATTGGATGATGTTATGGAGGAGATTGGGTTGGGGCCAAATGGCGGTCTCATCTACTGCATGGAgtatcctgttatttaagcattatatttgtttattttataggctgccaaagctatgtaattgattagttctgaactaatgcacttctgctggtgcattttt...

Basic information

species Zea mays
transcript GRMZM2G131324_T01
intron # 4
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G131324_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g50620.2 (Oryza sativa), 5'ss of exon 3
ATATCAGAGAGCTGATTTCATTGGATGATGTTATGGAGGAGATTGGGTTGGGGCCAAATGGCGGTCTCATCTACTGCATGGAgtatcctgttatttaagcattatatttgtttattttataggctgccaaagctatgtaattgatt--agttctgaactaatgcacttctgctggtgcattttt------
|||| || ||||| || |||||||||||||| ||||||||  ||||| |||| ||||||||||| || ||||| |||||||||||||||||| |   | ||||   | | || |||||||    | ||    || |  |    | |  |||| | |||| |  | |||||| |     ||||        
ATATTAGGGAGCTCATATCATTGGATGATGTCATGGAGGAACTTGGGATGGGACCAAATGGCGGGCTTATCTATTGCATGGAgtatcctgtttt---aacattgagtcttttaattttat---ttcccttttctttccaggctacttaagttattaactga--cccttctggtaaattatttgcaatgtg

upper sequence: GRMZM2G131324_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g21914.1 (Oryza sativa), 5'ss of exon 3
ATATCAGAGAGCTGATTTCATTGGATGATGTTATGGAGGAGATTGGGTTGGGGCCAAATGGCGGTCTCATCTACTGCATGGAgtatcctgttat------ttaagcattatatttgtttattttataggctgccaaagctatgtaattgat--tagttctgaactaatgcacttctgctggtgcattttt
|||| || ||||| || |||||||||||||| ||||||||  ||||| |||| ||||||||||| || ||||| |||||||||||||||||| |      || |   ||||     |||  |||  | |||    ||| | | ||| ||||  | ||  | || || |     | ||||| ||       
ATATTAGGGAGCTCATATCATTGGATGATGTCATGGAGGAACTTGGGATGGGACCAAATGGCGGGCTTATCTATTGCATGGAgtatcctgttttgagtcttttaattttattgcccttttctttccaagctatttaagttct-taactgatccttgtggtaaattatttgcaatgtgctgttg-------

upper sequence: GRMZM2G131324_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA08G39880.1 (Glycine max), 5'ss of exon 4
ATATCAGAGAGCTGATTTCATTGGATGATGTTATGGAGGAGATTGGGTTGGGGCCAAATGGCGGTCTCATCTACTGCATGGAgtatcctgttatttaagcattatatttgtttattttataggctgccaaagctatgtaattgattagttctgaactaatgcacttctgctggtgcattttt---
|||| || || || |||||  | |||||||||||||||||  |||| ||||| || ||||| |||||  |||||||||||||||||||| || ||| |  |   |  |||| |||||| |   |  ||     |     | |||||   |||  | |  ||   |   ||||    |  |     
ATATAAGGGAACTCATTTCCCTAGATGATGTTATGGAGGAACTTGGATTGGGTCCTAATGGTGGTCTTGTCTACTGCATGGAgtatccttttttttga--agggttgttgtctattttctttacaaccttctttgaaacagtgattt-ctcttcattgttgttttcaggctgccttaagtagaga

upper sequence: GRMZM2G131324_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv00s0174g00200.t01 (Vitis vinifera), 5'ss of exon 3
ATATCAGAGAGCTGATTTCATTGGATGATGTTATGGAGGAGATTGGGTTGGGGCCAAATGGCGGTCTCATCTACTGCATGGAgtatcctgttatttaagcattatatttgtttattttataggctgccaaagctatgtaattgattagttctgaactaatgcacttctgctggtgcattttt---------------------------
|||| || |||||  |||| ||||||||||||||||||||| ||||  ||||||||||||| || || || |||||||||||||||||| ||  ||  ||||| ||||| ||| | ||  |   |     | |  | ||  ||||  |||   |     ||   ||  |  |||| || |||                           
ATATTAGGGAGCTTGTTTCCTTGGATGATGTTATGGAGGAGCTTGGACTGGGGCCAAATGGTGGCCTTATGTACTGCATGGAgtatccttttccttt-gcattttatttatttgtatttaaatatttttcatccttttagatgat--gttgctagt---tgtttttgcgaaggtgtatgttttgaatgaccttacatctcagcaattag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|67031739|gb|CO460488.1|CO460488
EST:     ATGGAGGAGATTGGGTTGGGGCCAAATGGCGGTCTCATTTACTGCATGGA                         GCACCTTGAAGACAGCTTGGATGATTGGTTTGATGAACAGCTAGAGAACTA
genomic: ATGGAGGAGATTGGGTTGGGGCCAAATGGCGGTCTCATCTACTGCATGGAgtatcctgtt ... aaaacctcagGCACCTTGAAGACAGCTTGGATGATTGGTTTGATGAACAGCTAGAGAACTA
EST: gi|32931459|gb|CF036271.1|CF036271
EST:     ATGGAGGAGATTGGGTTGGGGCCAAATGGCGGTCTCATTTACTGCATGGA                         GCACCTTGAAGACAGCTTGGATGATTGGTTTGATGAACAGCTAGAGAACTA
genomic: ATGGAGGAGATTGGGTTGGGGCCAAATGGCGGTCTCATCTACTGCATGGAgtatcctgtt ... aaaacctcagGCACCTTGAAGACAGCTTGGATGATTGGTTTGATGAACAGCTAGAGAACTA
EST: gi|26456742|gb|CA828325.1|CA828325
EST:     ATGGAGGAGATTGGGTTGGGGCCAAATGGCGGTCTCATCTACTGCATGGA                         GCACCTTGAAGACAGCTTGGATGATTGGTTTGATGAACAGCTAGAGAACTA
genomic: ATGGAGGAGATTGGGTTGGGGCCAAATGGCGGTCTCATCTACTGCATGGAgtatcctgtt ... aaaacctcagGCACCTTGAAGACAGCTTGGATGATTGGTTTGATGAACAGCTAGAGAACTA
EST: gi|32934477|gb|CF039289.1|CF039289
EST:     ATGGAGGAGATTGGGTTGGGGCCAAATGGCGGTCTCATTTACTGCATGGA                         GCACCTTGAAGACAGCTTGGATGATTGGTTTGATGAACAGCTAGAGAACTA
genomic: ATGGAGGAGATTGGGTTGGGGCCAAATGGCGGTCTCATCTACTGCATGGAgtatcctgtt ... aaaacctcagGCACCTTGAAGACAGCTTGGATGATTGGTTTGATGAACAGCTAGAGAACTA

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATCAGAGAGCTGATTTCATTGGATGATGTTATGGAGGAGATTGGGTTGGGGCCAAATGGCGGTCTCATCTACTGCATGGAgtatcctgttatttaagcattatatttgtttattttataggctgccaaagctatgtaattgattagttctgaactaatgcacttctgctggtgcattttt

- - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA